What is the difference between HISAT2 index "genome.tran" and "genome"

Question

[Chevy Xu]

I try to use HISAT2 in order to map the reads to the genome, while HISAT2 pre-index the genome for users.

I saw that alternative sequences will affect the mapping results, does genome.tran index includes the alternative splicing and alternative sequences compare with genome index?

And what the difference between index genome and genome_tran?

which index file should I use in mapping process?

1. genome

2. genome_tran

3. genome_snp_tran

Thanks for your answering

[li.anlin666]

这要看你想要达到什么目的，要是单纯的比对，就用第一个 Genome的Indexes就好。

[GenoMax]

Please post using English alphabet, otherwise this post may be deleted.

[Ram]

Google Translate says

Answer 1

[WouterDeCoster]

From https://ccb.jhu.edu/software/hisat2/index.shtml

• genome: HFM index for reference
• genome_snp: HGFM index for reference plus SNPs
• genome_tran: HGFM index for reference plus transcripts
• genome_snp_tran: HGFM index for reference plus SNPs and transcripts

[lakhujanivijay]

For a typical RNA-seq analysis, how do I decide which one to use? It surely depends on what I am looking for but I am not able to figure out. Can you please provide some hints?

[vermack]

You will likely need the genome_tran.

[Arindam Ghosh]

Does genome not contain any info on snp/transcripts?